There are two ways to control the amount of seat tube or head tube extending above the top of the top tube and the amount of head tube extending below the bottom edge of the down tube. Which way the extension is controlled is chosen in the Primary dimensions dialog box 
. The first method is to enter the amount of extension measured along the edge of the tube as indicated by the red mark on the three icons shown here 
, 
, 
. Alternatively, clicking on any of these three icons will toggle the control to the intersections of the centerlines as indicated by the red marks shown here 
, 
, 
. If we toggle back to the edge method and look closely at the dimension for head tube extension above the top tube, we can see that this extension is being controlled by a 10mm dimension. This means that as long as we leave this dimension set to 10mm, no matter how we change the frame geometry in the future, there will always be exactly 10mm of head tube extending above the top edge of the top tube. We can see this as we change the angle of the top tube. The dimension locating the intersection of the centerlines will change but the dimension defining the amount of extension along the edge will remain constant. Meanwhile, if we toggle the control in order pin the tubes at the intersection of the centerlines, then as we change the top tube angle, it will be the centerline dimension that remains constant, while the amount of extension measured along the edge will change. This behaviour also holds for the interestions of the top tube and seat tube as well as the intersection of the down tube and head tube.
There is one special case to be aware of. To illustrate this point, I will switch back to the edge extension method. Notice that if you choose to curve any of the tubes in the main triangle, BikeCAD will switch to pinning the tubes at the intersections of the centerlines. BikeCAD will remain locked in this setting until there are no longer any curved tubes in the main triangle. Be careful if you ever do accidentally check any of the curved tubes check boxes in the Tubing dialog box 
as this will toggle the settings in the Primary dimensions dialog box and it will be up to you to switch back to the edge extension method if that is your preference.